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B
IOCONDUCTOR
/
CA
BIG


Adopter Installation Guide



caBIG


is an initiative of the National Cancer Institute, NIH, DHHS

Updated
December 9, 2013


Table of Contents


Introduction

................................
................................
................................
................................
.................

1

Overview of Bioconductor / caBIG

................................
................................
...............................

1

Bioconductor / caBIG Minimal System Requirements
................................
................................
............

1

Minimal System Requirements

................................
................................
................................
....

1

Bioconductor / caB
IG Software and Technology Requirements

................................
............................

2

Software Requirements

................................
................................
................................
.............................

2

Required Software

Not Included in the Bioconductor / caBIG

................................
.............

2

Optional Software

................................
................................
................................
...........................

3

Upgrading to Bioconductor / caBIG from Previous Bioconductor / caBIG Versions

.........................

5

Installing Bioconductor / caBIG

................................
................................
................................
................

5

Preliminary Considerations

................................
................................
................................
.......................

5

Bioconductor / caBIG Object
Model

................................
................................
................................
.......

5

Downloading Bioconductor / caBIG
................................
................................
................................
.........

5

Executing Tests
................................
................................
................................
................................
............

8

Tes
ting RWebServices and SJava configuration

................................
................................
......................

9

Testing RWebServices and Exemplar functionality

................................
................................
.................

9





Bioconductor/caBIG

Installation Guide



1


Introduction


Overview of
Bioconductor/
caBIG

Bioconductor is an

open source statistical
software project consisting of over 200
user
-
contributed packages;
Bioconductor
/caBIG

exposes functionality of three of
those modules (for microarray pre
-
processing, DNA copy number variation,
and SELDI
-
TOF mass spectroscopy peak
identification) as
web services on a
caGrid node.




Bioconductor/caBIG Minimal

System Requirements


Minim
al

S
ystem
R
equirements



32
-

or 64
-
bit Linux systems with storage and memory r
equirements
proportional to data object size.



Bioconductor/caBIG adoption has been tested on the platforms shown in
Table
1
.




Linux Server

Model

Virtual Server 2005 R2
inside Microsoft Windows
Server 2003

CPU

X86_64, i686

Memory

1GB

Local
Disk

128GB


OS

CentOS 4.4 (RHEL
-
based)


Table
1

Platform Testing Environment






Bioconductor/caBIG

Installation Guide



2


Bioconductor / caBIG Software

and Technology
Requirements

Software Requirements

Required
Software

Not
Included in the
Bioconductor/
c
aBIG package

You must download and install required software that is not included with
Bioconductor/caBIG

(listed in
Table
2

). The software name, version,
description, and URL hyperlinks (for download) are indicated in the table.


Note that the versions we use differs a bit from the developer version. We
intentionally select the mainstream stable version of related software
instead of going for the developer non
-
stable version. However, because
software continues to evolve, we wi
ll continue to test future stable versions
when they come out.



(Required software that

is

included with
the Bioconductor / caBIG

is listed in Appendix I on
page
Error! Bookmark not defined.
.)

Software
Name

Version

Descript
ion

URL

Java
Development
Kit 5.0
update 9

j2sdk1.5.0_09

or higher

The J2SE
Software
Develop
ment
Kit (SDK)
supports creat
-
ing J2SE
applications

http://java.sun.com/j2se/1.5.0/ download.html

Ant

1.7.0

Java build
environment
tool

http://ant.apache.org

Apa
che
Tomcat

5.0.30

Servelet
container

http://tomcat.apache.org/download
-
55.cgi#5.0.30

ActiveMQ

4.1.0

Java
-
based
Message Bus

http://www.activemq.org

R

2.5.0
(development
release as of
3/1/2007)

R statistical
programming
language.
Additional
components
requ
ired by R
specified in R
installation and
administration
manual

http://cran.fhcrc.org/

http://cran.fhcrc.org/doc/manuals/R
-
admin.html

Bioconductor

2.0
Bioconductor
http://bioconductor.org





Bioconductor/caBIG

Installation Guide



3


Software
Name

Version

Descript
ion

URL

(development
release as of
3/1/2007)

software
packages

TypeInfo

1.0.0

Bioconductor
package for
specifying
function and
argument type

Details below

SJava

0.69
-
4

Bioconductor
package for
Java/R
interface

Details below

Apache Axis

1.4

SOAP
implementation
(required for
deployment as
web service)

http://www.apache.org/dyn/closer.cgi/ws/axis/1_4/

Globus
Toolkit

4.0.3

Distributed
computing
infrastructure
(required for
deployment as
grid service)

http://gforge.nci.nih.gov/frs/download.php/1334/ws
-
core
-
enum
-
4.0.3.zip

caGrid

1.0

Infrastructure
for caBIG on
Globus
(required for
deployment as
grid service)

http://gforge.nci.nih.gov/frs/download.php/1450/caGrid
-
1.0_Installer.jar

Table
2

Required software and technology for
Bioconductor /
caBIG

Optional
Software

Optional software to

use with
Bioconductor/caBIG

is listed in
Table
3
.
The
included (
Incl
.) column indicates (with a
Yes
) if the software is packaged
with the SDK.
No

indicates that you must supply the software. A hyperlink
is included for your refer
ence to appro
priate sources.


Software
Name

Version

Description

URL

Incl.

JUnit

4.1

Unit testing framework

http://prdownloads.sourcef
orge.net/junit/junit4.1.zip?d
ownload

Ye
s





Bioconductor/caBIG

Installation Guide



4


RUnit

0.4.14

Unit testing framework

Details below

No

Table
3

Optional software and technology for the
Bioconductor / caBIG






Bioconductor/caBIG

Installation Guide



5


Upgrading to Current Release of
Bioconductor/caBIG
from
Previous
Bioconductor/caBIG
Versions

There is n
o previous version of Bioconductor/caBIG.


Installing
Bioconductor/caBIG



Preliminary Considerations


BEFORE YOU
BEGIN


Bioconductor/caBIG

has been tested with the operating systems and
hardware specified on
pages
1

through
3
of this guide. We choose to run
the
Bioconductor/caBIG

node on a virtual machine for ease of future
migration, dynamic resource allocation when needed, and minimization of
hardware dependencies. We use a particular implementation of virtual
machine (Vi
rtual Server 2005) running inside Windows Server 2003. The
installation is expected to work in other VM environment (such as VMWare)
or non
-
VM hosts. Instruction of VM setup is not included here.

For the guest OS that is running
Bioconductor/caBIG
, we ch
oose CentOS 4.4
because it is a mainstream RHEL
-
based system with mature packaging
and patching mechanism in place while being still available to the general
public. Other Linux distributions are expected to work, but the detailed
packaging and patching m
echanism might be different.




Bioconductor/caBIG Object Model

NOTE:




The object models used by Bioconductor are available at
http://tinyurl.com/2aqgf3



Downloading Bioconducto
r/caBIG


SUGGESTION

To best understand the installation and testing procedures
for
Bioconductor/caBIG
,
it is recommended that you follow the proce
dures
described in this section with minimal deviation.





Bioconductor/caBIG

Installation Guide



6





Complete the following steps to download and i
nstall
Bioconductor/caBIG:


Step

Action

1

General OS setup and patching. We choose the default minimal server
configuration during setup. Updating and installing dependent packages
are performed

by both up2date and yum (preferred).


For compatibility reasons, SELinux is disabled.


For the Apache Ant/Tomcat/Axis and JDK installation, we choose the
jpackage solution (
http://www.jpackage.org
) for ease of
maintenance and
management. Instructions on adding the jpackage repository is available
from
http://www.jpackage.org/yum.php
. However, installation of the above
packages from source should also work.


2

I
nstall, if necessary, the Java Software Development Kit, following
instructions at the web site indicated above.

Ensure that the JAVA_HOME environment variable is set, and that your
PATH environment variable includes path to the Java binary, using
instruc
tions at the Java Software Development Kit installation site.

3

Install, if necessary, Ant, following instructions at the site indicated above.

Ensure that the ANT_HOME environment variable is set and that your
PATH environment variable includes path to
the Ant batch file, using
instructions at the Ant installation site.

4

Install, if necessary, ActiveMQ, following instructions at the site indicated
above.

Ensure that the JMS_HOME environment variable is set.

e.


Configure the ActiveMQ broker to use non
-
pe
rsistent messages. Do this
by finding the <broker useJmx=”true”> tag in the file


JSM_HOME/conf/activemq.xml


And adding the attribute



<broker useJmx="true" persistent="false">

f.


5


Install, if necessary, Apache tomcat and
(if deploying as web service)
Apache axis. Ensure that the apache
-
axis/webapps/axis folder is copied

to
apache
-
tomcat/webapps/axis.

Ensure
that the environment variable CATALINA_HOME points to the
installation directory of apache
-
tomcat.





Bioconductor/caBIG

Installation Guide



7


Step

Action

5

Install, if necessary, R for your platform. I
t is best to do this from source,
by visiting
http://cran.fhcrc.org

and following the “Manuals” and then “R
Installation and Administration” links.
=
1.

Download:
R
-
2.5
.0.tar.gz

from
the site indicated above, by following
the Sources link and saving the file to disk.

2.

Unpack the source to a temporary location (such as /tmp) with


tar xzf R
-
2.5
.0.tar.gz

3.

Create a directory for installation
and change to this directory
, e.g.,


mkdir ~/TOP_DIR/R
-
2.5.0

cd ~/TOP_DIR/R
-
2.5
.0

4.

Config
ure to enable shared libraries (and other relevant options
--

read
the R Installation and Administration manual for details)


/path/to/tmpLocation/R
-
2.5.0/
configure
--
enable
-
R
-
shlib

5.

Make the R binary distribution


make

Ensure that the R_HOME environment va
riable is set and that your PATH
environment variable includes R, using instructions at the R installation
site.

Ensure that R is configured to correctly identify the intended Java system.
On Linux, execute the command

grep JAVA $R_HOME/Makeconf

JAVAC

shou
ld be defined; use the command

R CMD javareconf

to re
-
configure

$R_HOME/Makeconf

(e.g., after correcting JAVA_HOME
to point to the location of the JDK) without re
-
installing R.

6

Install Bioconductor, following instructions at the site indicated above. In

brief, launch an R session by typing R at the command prompt. In R, type
the following (‘>’ is the R prompt)
=
By=摥f慵ltI=灡ckag敳⁡re=i湳瑡nl敤=i渠獹獴em
J
wi摥=li扲慲y=l潣oti潮=獯⁡sl=
畳ur猠桡v攠慣捥獳st漠t桥m.
=
=
> source(

http://bioconductor.org/biocLite.R

)

> biocLite()

Exit R with the command
q()

7

Obtain and install TypeInfo and additional packages. From the command
line, launch R and enter the following commands:


>
source(“http://bioconductor.org/biocLite.R”)

> biocLite(c(“TypeInfo”, “DNAcopy”, “PROce
ss”))





Bioconductor/caBIG

Installation Guide



8


Step

Action

8

Obtain and install
RUnit
. From the command line, launch R and enter the
following commands:


source(“http://bioconductor.org/biocLite.R”)

biocLite(“RUnit”)


9

Obtain and install SJava.

To install SJava on linux, execute the command (typed on a s
ingle line)

R CMD INSTALL
--
configure
-
vars=”CFLAGS=
-
fPIC”
--
clean
SJava_<vers>.tar.gz

Follow the instructions in the output to set the environment variable

LD_LIBRARY_PATH

10

Obtain and install Bioconductor/caBIG RWebServices.

To install RWebServices on
linux, execute the command (with <vers>
replaced by the current version number)

R CMD INSTALL
--
clean RWebServices
_<vers>.tar.gz


11

Obtain and install desired Biocondcutor/caBIG modules. The modules
normally come with a ca
-

prefix. Install modules using


R CMD INSTALL
--
clean
<module>_<vers>.tar.gz


12


(Optional)

To streamline the updating and installation of the associated R packages,
we set up a nightly cron job to check out the source from the subversion
repository, compile and install. Subsequent

tests are run to confirm the
validity of the newer packages. We do not recommend this for production
and stable use.

13

Install, if necessary, caGrid 1.0, following instructions at
http://gforge.nci.nih.gov/frs/download.php/1454/caGrid
-
1.0_Installer_Instructions.pdf


http://www.cagrid.org

is also a great resource for tutorial.


caGrid comes with its own distributio
n of ant, tomcat and globus toolkit.
By default it installs into user’s home diretory. Change them to the system
wi摥=摩r散瑯eyI=獵捨=a猠/畳爯l潣ol/獨sr支捡gri搮==te=獵杧敳t=捯浰cli湧=a湤=
r畮湩湧=捡dri搠畳dn朠楴猠潷渠摩獴ri扵ti潮=to=mi湩miz攠捯e灡ti扩lit
y=i獳略献==
Al獯Ⱐt桥=捡dri搠楮str畣ti潮=i猠ti湤潷s
J
潮lyI=扵t=w攠桡e攠v敲楦i敤=t桡t=it=
w潲o猠畮摥r=䱩湵xI=t潯.=
=

=
a数l潹=Bi潣o湤畣瑯u=灡ckag敳=潮=捡cri搠畳dng=fntr潤畣u:
=
=
cd $CAGRID_HOME

ant introduce


Executing Tests

Tests
must be
performed to make sure your system is functioning properly. Perform the
following system tests to verify a successful installation.





Bioconductor/caBIG

Installation Guide



9



Testing RWebServices and SJava
configuration

Perform the following steps to test the
RWebServices and SJava
configuration:


Step

Action

1

Unpack the test scripts. To do this, enter the following
commands

library(RWebServices)

unpackAntScript(“/path/to”)

Replace ‘/path/to’ with a path that is convenient for you. This will create
fil敳=扵il搮dmlI=ote打敲vi捥獅nv.灲潰敲pi敳=慮d
=
ot敢pervi捥獔畮i湧.灲潰敲ei敳

=
Alter湡tiv敬yI=數散et攠e桥=獨sll
=
捯浭慮d=(敮ter=潮=愠獩agl攠汩湥I=獩湧le=慮搠摯畢l攠q畯t敳=慲a=im灯rt慮t)
=
=
echo "library(RWebServices);
unpackAntScript('/path/to')" | R
--
vanilla

2

Check basic configuration
. To do this, at

the command line, change to the
directo
ry /path/to

and run the command

ant basic
-
prop

Confirm that the

variables are reasonable. If the output contains a line


[echo] sjava configuration? WARNING! please run 'ant
recompile
-
sjava'

...

then it is necessary
to evaluate the command

ant recompile
-
sjava

3

Run JUnit tests with the command

ant rservices
-
test


Testing RWebServices and Exemplar functionality

Perform the following steps to test
exemplar functionality
:


Step

Action

1


In the directory created above
, execute the following command

ant map
-
package

Dpkg=<module>

ant unpack
-
package

Dpkg=<module>

ant precompile





Bioconductor/caBIG

Installation Guide



10


Step

Action

2

In a second shell window, navigate to the directory created above and
initialize the web services environment, e.g.,

${CATALINA_HOME}/bin/sta
rtup.sh

${JMS_HOME}/bin/activemq&

ant start
-
worker&

3

Return to the original shell, and execute tests with

ant local
-
test

Test output is in the
test/output

directory.

4

Shut down the web services environment with the following commands


${JMS_HOME}/bin/a
ctivemq stop

${CATALINA_HOME}/bin/shutdown.sh


Error messages generated from the worker, as it losses contact with
activeMQ and terminates, can be safely ignored.